Extended Data Fig. 4: Cell-type composition of SUV420H1+/− and isogenic control organoids.
From: Autism genes converge on asynchronous development of shared neuron classes
a, Immunohistochemistry of Mito210 SUV420H1+/− and control organoids cultured for one month (35 d.i.v.). Optical section from the middle of whole-organoid dataset. Scale bars are 500 μm. SOX2, a marker of neuronal progenitors, is shown in red, and nuclei (Syto16) are shown in blue. b, Immunohistochemistry for the postmitotic excitatory neuronal marker TBR1 and GABAergic marker DLX2 in Mito294 control and SUV420H1+/− organoids at one month (35 d.i.v.). Scale bars: 200 μm. c–e, scRNA-seq data from one month (Mito294 35d.i.v. (c), PGP1 35 d.i.v. (d) and Mito210 28 d.i.v., batch I (e)) control and SUV420H1+/− organoids. Bar charts show the percentage of cells for all the cell populations in each control and mutant organoid. Adjusted p-values for a difference in cell type proportions between control and mutant, based on logistic mixed models (see Methods) are shown. f, scRNA-seq data from Mito210 35 d.i.v. (batch II) control and SUV420H1+/− organoids. Left top shows combined t-SNE plots of control and mutant organoids (n = 3 single organoids per genotype). Cells are coloured by cell-type, and the total number of cells per plot is indicated. Left bottom, t-SNE plots for control and mutant individual organoids. Immature deep-layer projection neuron populations are highlighted in colour. Right, bar charts show the percentage of cells for all the cell populations in each control and mutant organoid, as in c–e. g, Enriched GO terms for genes upregulated and downregulated in SUV420H1+/− vs. control across lines. Genes were calculated using cells from the partition of interest. The top 5 most significant terms per dataset are shown. Size of dot indicates the proportion of genes belonging to each term found in the list of dysregulated genes (“GeneRatio”). Colour indicates enrichment adjusted p-value. Numbers in parentheses along the y axis indicate the number of DEGs in that dataset. As control, we calculated GO term enrichment for 100 random gene sets of the same size sampled from genes expressed in each dataset, and found no significant enrichment of these terms (see Methods). Number of organoids used for each analysis can be found in the Methods under “Statistics and reproducibility”. aRG, apical radial glia; DL, deep layer; UL, upper layer; PN, projection neurons; oRG, outer radial glia; IPC, intermediate progenitor cells; CPN, callosal projection neurons; CFuPN, corticofugal projection neurons; GABA N, GABAergic neurons.
